Challenges in microbiological identification

Challenges in microbiological identification

By Julie Archer - 26 April 2016

Julie Archer, Microbiologist discusses some of the common issues and challenges in microbiological identification and the sophisticated DNA-based methods being used at Campden BRI to help food and drink companies.

What are the commonest microbiological issues you get asked to help with?

Microbiological issues can affect many different foodstuffs – so this is wide-ranging. One of the common areas we investigate is spoilage. This can be triggered by an issue at the production site or in the distribution chain. We identify the cause so the manufacturer can take steps to prevent it happening again.

Another example would be the rise in enquiries relating to the detection of Shigella Toxin-producing E. coli. (STEC), particularly for sprouted seeds, due to EU legislation which requires sprouted seeds to be analysed for 6 STEC serotypes (O157, O145, O111, O103, O26 and O104:H4) prior to release onto the market.

What are some of the biggest microbiological challenges facing the food industry?

Campylobacter is considered to be responsible for more than 280,000 cases of food poisoning each year in the UK alone. Poultry is one major source of Campylobacter. Many producers and manufacturers ask for our help to determine if the interventions they have put in place to control Campylobacter are effective.

Pathogenic viruses are an emerging problem. The UK Government’s Advisory Committee on the Microbiological Safety of Food (ACMSF) suggests that the most important viruses associated with food borne infection are Norovirus, Hepatitis A and Hepatitis E. Although they cannot grow on or in foods, viruses are carried by foods. Viruses cannot be easily cultured outside of their host cells, so we have developed sensitive molecular methods to detect the presence of their viral genome (virus RNA).

How have microbiological analysis techniques changed over the years?

Advances in DNA technology have made detection and identification of microorganisms faster, more sensitive and more specific. We use a suite of DNA-based methods, including sensitive PCR methods, which we have developed to detect viruses and STEC. We are also using DNA fingerprinting methods to help manufacturers pinpoint the source of outbreaks of bacterial contamination, so that recurrence can be prevented.

Moving into the next era of microbiology, we are actively exploring the application of ‘next generation sequencing’ to the food industry. We are working in collaboration with other experts in the field to develop new services in this area. Among the speakers at our “Understanding microbial genomes and ‘next generation’ sequencing” seminar on 20 May is Dr Steven Musser, Deputy Center Director Scientific Operations at the FDA, who will be giving a US perspective on next generation sequencing.

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